gplots protocols

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gplots specifications

Information


Unique identifier OMICS_22070
Name gplots
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.0.1
Stability Stable
Requirements
stats, grid, gtools, MASS, KernSmooth, caTools, gdata, R(≥3.0)
Source code URL https://cran.r-project.org/src/contrib/gplots_3.0.1.tar.gz
Maintained Yes

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  • person_outline Gregory Warnes <>
  • person_outline Gregory Warnes <>

gplots in pipelines

 (157)
2018
PMCID: 5761711
PMID: 29295970
DOI: 10.12659/MSM.905410

[…] of 2024 differentially expressed mrnas and 198 mirnas were identified by the “deseq” package in r. then, the heat map with complete linkage clustering of demrnas and demirnas was built using the “gplots” package in r. (, ). as a result, there were 1042 (51.48%) up-regulated and 982 (48.52%) down-regulated degs. moreover, a total of 158 (79.79%) up-regulated and 40 (20.21%) down-regulated […]

2018
PMCID: 5776392
PMID: 29387063
DOI: 10.3389/fimmu.2017.02004

[…] log2fc ≤ −1.0 (downregulated) are considered to be differentially expressed. venn diagrams were drawn using the differentially expressed genes between the populations. heat maps were drawn using the gplots package on the differentially expressed genes between mampc and c-mo populations. a clustering method was set to complete and distance measure to pearson correlation., we isolated total rna […]

2018
PMCID: 5797686
PMID: 29441023
DOI: 10.3389/fphys.2018.00019

[…] usa, www.graphpad.com., cel files were analyzed with rstudio (rstudio team, ) (version 0.99.903), r (r development core team, ) (version 3.2.5) and various r-packages (e.g., “affy,” “pvclust,” “gplots,” and “factominer”). for a complete list of the packages including version numbers and citations, please refer to supplement ., pathway analysis was carried out with cluego (bindea et al., ) […]

2018
PMCID: 5919721
PMID: 29620157
DOI: 10.3892/ijo.2018.4336

[…] analysis. principal component analysis (regularized log-transformed, sizefactor-corrected counts obtained from deseq2), and data visualization were performed in r (version 3.4.0) using the packages gplots, ggfortify, genefilter and rcolorbrewer., based on the ngs data, differentially regulated cellular mirnas were validated by rt-qpcr. first, 111 ng of rna were reverse transcribed in triplicate […]

2018
PMCID: 5928165
PMID: 29712898
DOI: 10.1038/s41467-018-03590-5

[…] out using cufflinks software. differential gene expression analyses between groups were performed using htseq software for tumor samples and deseq2 software for cell line samples. heatmap.2 in the ‘gplots’ package of the r program was used for the construction of heat maps. genes that were up- or downregulated in both c13* and skov3 cells with a p value of less than 0.05 were analyzed using ipa […]


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gplots in publications

 (1352)
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] clustering of the samples the rlog normalization in deseq2 was applied. we used the r library pheatmap for sample clustering (euclidian distance, complete linkage clustering) and heatmap.2 from the gplots package to visualize differentially expressed genes (pearson correlation and ward.d clustering)., total rna was isolated using rneasy mini kit (qiagen). reverse transcription was performed […]

PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18

[…] (pcoa) plots, and microbial network maps. metagenomic function was predicted using picrust () online galaxy version by the method of umu et al. (). heat maps were generated using calypso and gplots package in r., the white’s nonparametric t test and kruskal-wallis h test were performed to compare the relative abundance of genera for two groups and more than three groups, respectively. […]

PMCID: 5952419
PMID: 29764370
DOI: 10.1186/s12879-018-3127-4

[…] package in r [] was used to normalize the counts and call differential expressions. principal component analysis (pca) was used for data visualization. hierarchical clustering was performed with the gplots package in r. the roc curve was plotted with the proc package in r. functional and network analyses of differentially expressed genes were performed using ingenuity pathway analysis (ipa, […]

PMCID: 5951829
PMID: 29760381
DOI: 10.1038/s41419-018-0622-x

[…] 5, we also built up heatmaps for genes annotated different gene ontology terms about aging, cell proliferation or cell cycle, or for genes known as hepatocellular carcinoma markers using r package gplots. similarly, all these heatmaps showed that the gene expression profiles in c 8w + a 4w group were separated with which in c 8w and c 12w, and the profilers in c 8w and c 12w were clustered […]

PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] we used rsem’s transcript per million (tpm) tables; to compare with literature, we used fragment per kilobase mapped reads (fpkm) tables., visualization: the data was visualized using the r packages gplots, ggplot2, and markdown reports., transcriptional analysis: single cells from female germ cells our dataset and from guo et al., 2015 (gene expression omnibus (geo) database gse63818) […]


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